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- PDB-1ojd: HUMAN MONOAMINE OXIDASE B IN COMPLEX WITH Lauryldimethylamine-N-o... -

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Basic information

Entry
Database: PDB / ID: 1ojd
TitleHUMAN MONOAMINE OXIDASE B IN COMPLEX WITH Lauryldimethylamine-N-oxide (LDAO)
ComponentsAMINE OXIDASE [FLAVIN-CONTAINING] B
KeywordsOXIDOREDUCTASE / FAD-CONTAINING AMINE OXIDASE / MAOB
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion / : / dopamine catabolic process / primary-amine oxidase / mitochondrial envelope / hydrogen peroxide biosynthetic process / response to corticosterone / substantia nigra development / response to toxic substance / flavin adenine dinucleotide binding / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / electron transfer activity / response to xenobiotic stimulus / dendrite / neuronal cell body / mitochondrion / identical protein binding
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBinda, C. / Edmondson, D.E. / Mattevi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Insights Into the Mode of Inhibition of Human Mitochondrial Monoamine Oxidase B from High-Resolution Crystal Structures
Authors: Binda, C. / Li, M. / Hubalek, F. / Restelli, N. / Edmondson, D.E. / Mattevi, A.
History
DepositionJul 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMINE OXIDASE [FLAVIN-CONTAINING] B
B: AMINE OXIDASE [FLAVIN-CONTAINING] B
C: AMINE OXIDASE [FLAVIN-CONTAINING] B
D: AMINE OXIDASE [FLAVIN-CONTAINING] B
E: AMINE OXIDASE [FLAVIN-CONTAINING] B
F: AMINE OXIDASE [FLAVIN-CONTAINING] B
G: AMINE OXIDASE [FLAVIN-CONTAINING] B
H: AMINE OXIDASE [FLAVIN-CONTAINING] B
I: AMINE OXIDASE [FLAVIN-CONTAINING] B
L: AMINE OXIDASE [FLAVIN-CONTAINING] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)598,52730
Polymers588,37710
Non-polymers10,15020
Water0
1
A: AMINE OXIDASE [FLAVIN-CONTAINING] B
B: AMINE OXIDASE [FLAVIN-CONTAINING] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7056
Polymers117,6752
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: AMINE OXIDASE [FLAVIN-CONTAINING] B
D: AMINE OXIDASE [FLAVIN-CONTAINING] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7056
Polymers117,6752
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: AMINE OXIDASE [FLAVIN-CONTAINING] B
F: AMINE OXIDASE [FLAVIN-CONTAINING] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7056
Polymers117,6752
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: AMINE OXIDASE [FLAVIN-CONTAINING] B
H: AMINE OXIDASE [FLAVIN-CONTAINING] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7056
Polymers117,6752
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
I: AMINE OXIDASE [FLAVIN-CONTAINING] B
L: AMINE OXIDASE [FLAVIN-CONTAINING] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7056
Polymers117,6752
Non-polymers2,0304
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)108.405, 132.431, 154.838
Angle α, β, γ (deg.)90.14, 90.45, 114.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.98619, -0.07844, 0.14584), (-0.07081, -0.59637, -0.79958), (0.1497, -0.79887, 0.58258)0.42503, -6.89186, -3.41873
2given(0.99489, 0.00721, 0.1007), (0.01354, -0.99796, -0.06231), (0.10005, 0.06336, -0.99296)-7.99658, 30.27496, 90.06601
3given(-0.96758, -0.15855, 0.19661), (0.0485, 0.64731, 0.76068), (-0.24787, 0.74555, -0.61864)-7.90396, 37.35556, 92.98945
4given(-0.02234, -0.39684, 0.91762), (-0.40219, -0.83673, -0.37165), (0.91528, -0.37736, -0.14091)74.33958, 10.70917, 40.91425
5given(0.18776, -0.49866, 0.84622), (0.40343, 0.82467, 0.39644), (-0.89554, 0.26695, 0.35602)73.89708, 17.59059, 44.38742
6given(0.33959, 0.41194, -0.84557), (-0.46187, 0.85617, 0.23162), (0.81936, 0.31189, 0.48101)-13.83994, 78.36705, 4.11747
7given(-0.48765, 0.39828, -0.7769), (0.43345, -0.662, -0.61145), (-0.75784, -0.63492, 0.15019)-13.62854, 71.46387, 0.79099
8given(-0.61241, 0.30915, -0.72758), (-0.38109, 0.69091, 0.61434), (0.69262, 0.6535, -0.30531)32.62793, 79.47947, 91.5071
9given(0.4699, 0.4369, -0.76702), (0.40775, -0.8781, -0.25037), (-0.7829, -0.1951, -0.59076)32.68354, 72.37494, 88.56023

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Components

#1: Protein
AMINE OXIDASE [FLAVIN-CONTAINING] B / MONOAMINE OXIDASE / MAO-B


Mass: 58837.730 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P27338, monoamine oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
Compound detailsFUNCTION: CATALYZES THE OXIDATIVE DEAMINATION OF AMINES CATALYTIC ACTIVITY: RCH2NH2 + H2O + O2 = ...FUNCTION: CATALYZES THE OXIDATIVE DEAMINATION OF AMINES CATALYTIC ACTIVITY: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 %(w/v)PEG40001reservoir
270 mMlithium sulfate1reservoir
3100 mMADA1reservoirpH6.5
42 mg/mlprotein1drop
58.5 mMZwittergent3-121drop
625 mMpotassium phosphate1droppH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 140447 / % possible obs: 98.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 3.9
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.3 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 3.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.201

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOS

1gos


Resolution: 3.1→40 Å / SU B: 20.461 / SU ML: 0.366 / Cross valid method: THROUGHOUT / ESU R Free: 0.443
RfactorNum. reflection% reflectionSelection details
Rfree0.26041 1408 1 %RANDOM
Rwork0.25221 ---
obs0.25232 139001 98.4 %-
Displacement parametersBiso mean: 40.203 Å2
Baniso -1Baniso -2Baniso -3
1-5.5 Å2-1.09 Å2-1.55 Å2
2---4.36 Å2-1.55 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39529 0 690 0 40219
Refinement
*PLUS
Rfactor Rfree: 0.26 / Rfactor Rwork: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.016
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.5

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